Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004047 aminomethyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the primary and specific catalytic activity of GcvT - the transfer of the aminomethyl group from the lipoyl-bound intermediate (on gcvH) to tetrahydrofolate, producing 5,10-methylene-THF and ammonia. [file:METEA/gcvT/gcvT-uniprot.txt, "aminomethyltransferase"; "N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+)"]. Falcon deep research independently confirms this is the conserved, core catalytic role of GcvT across bacteria and corroborates the products of the reaction. Supporting Evidence: file:METEA/gcvT/gcvT-deep-research-falcon.md transfers the aminomethyl group from the H-protein intermediate to THF, producing 5,10-methylene-THF and releasing NH3 file:METEA/gcvT/gcvT-deep-research-falcon.md is a core catalytic component of the glycine cleavage system
GO:0005960 glycine cleavage complex	IEA GO_REF:0000002	ACCEPT	Summary: GcvT is a component of the glycine cleavage complex, working together with gcvP, gcvH, and gcvL to catalyze the oxidative cleavage of glycine. This is the primary cellular location for the enzyme. [file:METEA/gcvT/gcvT-uniprot.txt, "Glycine cleavage system T protein"]. Falcon deep research confirms GcvT (the T protein) functions with the GCS P, H, and L proteins, with the H protein carrying the lipoyl-bound aminomethyl intermediate that GcvT acts on. Supporting Evidence: file:METEA/gcvT/gcvT-deep-research-falcon.md functions with GCS P, H, and L proteins; H protein carries the lipoyl-bound intermediate
GO:0006546 glycine catabolic process	IEA GO_REF:0000002	ACCEPT	Summary: GcvT catalyzes the final step of glycine catabolism via the glycine cleavage system, transferring the aminomethyl group to THF and releasing ammonia. This connects glycine degradation to the one-carbon pool. [file:METEA/gcvT/gcvT-uniprot.txt, "Glycine cleavage system T protein"]. Falcon deep research corroborates that by producing 5,10-methylene-THF, GcvT links glycine interconversion to the one-carbon folate pool, which in Methylorubrum extorquens AM1 feeds assimilation pathways including the serine cycle. Supporting Evidence: file:METEA/gcvT/gcvT-deep-research-falcon.md By producing 5,10-methylene-THF, GcvT links glycine interconversion to the one-carbon folate pool file:METEA/gcvT/gcvT-deep-research-falcon.md H4F-dependent enzymes help maintain high levels of intermediates needed to feed the assimilatory serine cycle
GO:0008483 transaminase activity	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: This is technically correct as GcvT transfers an aminomethyl group, but it's a somewhat misleading general term. The more specific term GO:0004047 (aminomethyltransferase activity) provides better functional annotation.
GO:0016740 transferase activity	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: This is a very general parent term for all enzymes that transfer functional groups. While technically correct, the more specific term GO:0004047 provides much better functional annotation.

Core Functions

GcvT catalyzes the final step of the glycine cleavage system, transferring the aminomethyl group from the lipoyl-bound intermediate (on gcvH carrier protein) to tetrahydrofolate (THF), producing 5,10-methylene-THF and releasing ammonia. The enzyme functions as a component of the glycine cleavage complex, working in concert with gcvP (P protein), gcvH (H protein), and gcvL (L protein) to catalyze the oxidative cleavage of glycine. In the context of methylotrophic metabolism, the glycine cleavage system connects the serine cycle to the THF one-carbon pool: glycine (produced from serine) is oxidatively cleaved, generating 5,10-methylene-THF that feeds into C1 metabolism, plus CO2 and ammonia. GcvT contains an aminomethyltransferase folate-binding domain and a C-terminal domain, and belongs to the GcvT family. The enzyme is essential for glycine catabolism and for recycling one-carbon units between amino acid metabolism and the THF-dependent one-carbon pool during methylotrophic growth.

Molecular Function:

aminomethyltransferase activity

Directly Involved In:

glycine catabolic process

In Complex:

glycine cleavage complex

Supporting Evidence:

file:METEA/gcvT/gcvT-uniprot.txt
aminomethyltransferase...Glycine cleavage system T protein...N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+)
file:METEA/gcvT/gcvT-deep-research-falcon.md
transfers the aminomethyl group from the H-protein intermediate to **THF**, producing **5,10-methylene-THF** and releasing **NH3**
file:METEA/gcvT/gcvT-deep-research-falcon.md
By producing **5,10-methylene-THF**, GcvT links glycine interconversion to the **one-carbon folate pool**
file:METEA/gcvT/gcvT-deep-research-falcon.md
functions with GCS **P, H, and L** proteins; H protein carries the lipoyl-bound intermediate

References

file:METEA/gcvT/gcvT-deep-research-falcon.md

Falcon deep research report for gcvT (C5AUG2) in Methylorubrum extorquens AM1

"transfers the aminomethyl group from the H-protein intermediate to **THF**, producing **5,10-methylene-THF** and releasing **NH3**"
"is a core catalytic component of the **glycine cleavage system**"
"functions with GCS **P, H, and L** proteins; H protein carries the lipoyl-bound intermediate"
"By producing **5,10-methylene-THF**, GcvT links glycine interconversion to the **one-carbon folate pool**"
"H4F-dependent enzymes help maintain high levels of intermediates needed to feed the assimilatory serine cycle"
"the THF-dependent one-carbon network and the GCS proteins are typically **cytosolic**"
"the AM1 GcvT is expected to be **cytosolic**"
"GcvT is also a core enzyme for the **reductive glycine pathway** used in synthetic C1 assimilation"

file:METEA/gcvT/gcvT-uniprot.txt

UniProt entry for gcvT aminomethyltransferase

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms.

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods.

Deep Research

Falcon

(gcvT-deep-research-falcon.md)

Research report: **gcvT** (UniProt C5AUG2) in *Methylorubrum extorquens* AM1 (METEA) Falcon Edison Scientific Literature 14 citations 2 artifacts 2026-06-03T06:53:33.155296

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000014 The requested panels from Figure 1 and Figure 5 are provided. The thermodynamic table from Figure 1c displays the reaction steps fo (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: gcvT (UniProt C5AUG2) in Methylorubrum extorquens AM1 (METEA)

Executive summary

The UniProt target (C5AUG2) is annotated as aminomethyltransferase (glycine cleavage system T-protein, GcvT; EC 2.1.2.10) from Methylorubrum extorquens strain AM1. Within the glycine cleavage system (GCS), GcvT is the tetrahydrofolate (THF)-dependent aminomethyl transferase that converts the aminomethylated intermediate carried by the lipoyl “swinging arm” of the H-protein into 5,10-methylene-THF while releasing ammonia, thereby linking glycine catabolism/synthesis to the cellular one-carbon (C1) folate pool. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

A key limitation of the available corpus retrieved here is that it contains little direct, AM1-specific experimental characterization of the particular AM1 protein sequence C5AUG2 (e.g., purified enzyme kinetics, mutant phenotypes in AM1). Accordingly, AM1-specific statements below are anchored to (i) the UniProt identity provided by the user and (ii) literature describing THF-dependent C1 metabolism in M. extorquens AM1 and the conserved GcvT function across organisms. (klein2022unravellingformaldehydemetabolism pages 4-5, wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

Recent work (2023) demonstrates that the reversible GCS module (including GcvT) can be engineered in cell-free formats to fix CO2 into amino acids with quantitative performance metrics (rates, yields, thermodynamic driving forces), highlighting real-world synthetic-biology applications of GcvT-containing systems. (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media 54c2569d, liu2023turnaircapturedco2 media d220b323)

1. Target verification and disambiguation (critical identity checks)

1.1 UniProt-provided identity (authoritative anchor)

The target protein is aminomethyltransferase / glycine cleavage system T-protein (GcvT), EC 2.1.2.10, encoded by gcvT in Methylorubrum extorquens AM1.

1.2 Gene symbol ambiguity management

The symbol gcvT is used broadly across bacteria for the GCS T-protein. All evidence used here refers to GcvT as THF-dependent aminomethyltransferase, consistent with the UniProt description; no evidence in the retrieved set suggested an alternative meaning of “gcvT” that would conflict with the UniProt identity. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23, liu2023turnaircapturedco2 pages 1-2)

2. Key concepts and definitions (current understanding)

2.1 The glycine cleavage system (GCS) and GcvT’s role

The GCS is a multi-protein enzyme system (classically P, H, T, and L proteins) that interconverts glycine and the one-carbon folate pool.

T-protein (GcvT; aminomethyltransferase; EC 2.1.2.10): transfers the aminomethyl group from the H-protein intermediate to THF, producing 5,10-methylene-THF and releasing NH3; this step is central to generating the activated C1 unit used in downstream metabolism. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

Mechanistically, the H-protein’s lipoyl arm cycles between reaction partners; the T-protein step produces a reduced form of the H-protein that must be re-oxidized (classically by L-protein), enabling subsequent catalytic cycles. (wittmiss2020stoichiometryoftwo pages 1-2)

2.2 Reaction chemistry and substrate specificity

At the functional level, bacterial GcvT enzymes are THF-dependent and act on the aminomethylated lipoyl arm of GCS H-protein, producing methylene-THF (5,10-CH2-THF) and releasing ammonia. (patel2016expressionofclostridium pages 20-23)

In the reverse direction (used in the reductive glycine pathway conceptually and in engineered systems), the GCS can produce glycine from 5,10-methylene-THF, CO2, and ammonium, coupled to reducing power. The reversibility of this module is a key conceptual basis for CO2/formate assimilation strategies. (wittmiss2020stoichiometryoftwo pages 1-2, liu2023turnaircapturedco2 pages 1-2)

2.3 Cellular localization

In bacteria, the THF-dependent one-carbon network and the GCS proteins are typically cytosolic, consistent with the biochemical role of GcvT acting on soluble THF and soluble protein partners (H/P/L). This is also consistent with the non-membrane-associated descriptions of the GCS in the cited sources. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

3. Organism context: Methylorubrum extorquens AM1 and C1 metabolism

M. extorquens AM1 is a model methylotroph that uses formaldehyde as a central intermediate during growth on methanol.

A 2022 review of formaldehyde metabolism notes that H4F/THF-dependent reactions occur in M. extorquens AM1 and that H4F-dependent enzymes help maintain high levels of intermediates needed to feed the assimilatory serine cycle, with formate described as a branch point between assimilation and dissimilation. This provides organism-level context that the THF one-carbon pool is an important metabolic hub in AM1, and therefore an enzyme that generates 5,10-methylene-THF (such as GcvT) is plausibly important for routing C1 units into central metabolism. (klein2022unravellingformaldehydemetabolism pages 4-5)

The same review emphasizes that AM1 relies heavily on the H4MPT-dependent pathway to keep formaldehyde below toxic levels (context for methylotrophy), while THF-dependent chemistry provides intermediates for assimilation. (klein2022unravellingformaldehydemetabolism pages 4-5)

Evidence gap: within the retrieved documents, there is no direct AM1 gcvT knockout/overexpression phenotype or purified AM1 GcvT kinetic characterization for UniProt C5AUG2.

4. Recent developments (prioritizing 2023–2024) and latest research

4.1 2023 (highly relevant): engineered reversible GCS for CO2-to-amino acid synthesis

A 2023 Nature Communications study developed an ATP- and NAD(P)H-free chemoenzymatic system that uses a re-engineered reversible GCS module (including T protein/aminomethyltransferase) coupled to non-enzymatic steps to synthesize glycine, serine, and pyruvate from methanol plus gaseous/air-derived CO2. (liu2023turnaircapturedco2 pages 1-2)

Key mechanistic insights include how the H-protein lipoyl/aminomethyl arm behavior (including “self-protection” within an H-protein cavity) affects overall performance; mutations that increase arm mobility improved glycine formation. Because the arm must commute between P and T proteins, these findings are directly relevant to how efficiently GcvT-containing modules can be engineered and optimized. (liu2023turnaircapturedco2 pages 5-7)

Thermodynamics for the overall glycine synthesis step were quantified, including how replacing the canonical L-protein/NADH reduction with DTT-based chemical reduction changes driving force. (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 media 54c2569d)

4.2 2024: limited direct GcvT-specific advances in retrieved set

Within the retrieved set, 2024 items referencing “aminomethyltransferase” were not focused on bacterial GcvT enzymology in Methylorubrum; thus, the most informative recent primary study available here is 2023. (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7)

5. Current applications and real-world implementations

5.1 Synthetic C1 assimilation (reductive glycine pathway) and pathway construction logic

The reductive glycine pathway concept leverages the reversibility of the GCS module to assimilate C1 units (e.g., formate/CO2) into biomass building blocks. In engineered contexts, GcvT is the THF-dependent module enabling conversion between glycine and 5,10-methylene-THF. (wittmiss2020stoichiometryoftwo pages 1-2, liu2023turnaircapturedco2 pages 1-2)

In an E. coli engineering study (2018), gcvT is explicitly identified as aminomethyltransferase and was included in synthetic operons constructed to enable the rGlyP in vivo. This demonstrates the standard engineering use of gcvT as the T-protein function in pathway design. (yishai2018invivoassimilation pages 6-8)

5.2 Cell-free biomanufacturing: CO2-derived amino acids

The 2023 study demonstrates a concrete “real-world” direction: cell-free or hybrid chemoenzymatic conversion of methanol and air-captured CO2 into amino acids at g/L levels by leveraging the GCS module (including GcvT). (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7)

6. Expert opinions and authoritative analysis (what the field considers important)

A consistent theme in the GCS literature is that the system’s multi-enzyme nature and intermediate channeling via H-protein complicate mechanistic and kinetic understanding. A 2022 in vitro study emphasizes that GCS kinetic data are scarce and that multi-protein stoichiometry can strongly affect rates, underscoring why GcvT function is often best understood in the context of the whole complex rather than as an isolated enzyme. (xu2022improvementofglycine pages 1-2)

In addition, multienzyme organization and subunit stoichiometry (demonstrated extensively in plants and also explored as a general property of GCS-like systems) supports the view that physical organization and partner availability influence the effective activity of GcvT in vivo. (wittmiss2020stoichiometryoftwo pages 1-2)

7. Relevant quantitative data and statistics (recent studies)

7.1 Thermodynamic and performance statistics for a GcvT-containing rGCS module (2023)

From Liu et al. (2023):

Overall glycine synthesis step (rGCS module): 5,10-CH2-THF + NH4+ + CO2 + NADH → glycine + THF + NAD+, with ΔrG′ ≈ −1.2 kJ/mol under the conditions described. (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 media 54c2569d)
Replacing the canonical reduction chemistry with DTT provides a more favorable overall driving force (e.g., DTT-based lipoic acid reduction step ΔrG′ ≈ −7.4 kJ/mol; redesigned glycine synthesis step with DTT ΔrG′ ≈ −8.0 kJ/mol). (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 media 54c2569d)
Glycine production rate optimized via engineered H-protein: up to ~75 μM/min at 60 μM engineered H (HM) vs <20 μM/min for wild-type H in their system context. (liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media d220b323)
Product titers and yields (formaldehyde + bicarbonate): 15.5 mM glycine (~1.2 g/L) in 3.5 h, with 78% carbon yield based on formaldehyde and 31% carbon yield based on CO2. (liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media d220b323)

These quantitative values describe a reconstituted/engineered GCS module containing T-protein activity, and therefore support expectations about what GcvT-containing systems can achieve, but they do not provide kinetic constants specific to the AM1 enzyme sequence C5AUG2.

8. Functional annotation narrative (for METEA gcvT / UniProt C5AUG2)

8.1 Molecular function

GcvT (aminomethyltransferase; EC 2.1.2.10) catalyzes THF-dependent transfer of an aminomethyl unit from the GCS H-protein intermediate to THF, generating 5,10-methylene-THF and releasing NH3; it is a core catalytic component of the glycine cleavage system. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

8.2 Biological process and pathway assignment

By producing 5,10-methylene-THF, GcvT links glycine interconversion to the one-carbon folate pool, which in methylotrophs like M. extorquens AM1 is connected to assimilation pathways (e.g., serine cycle feeding) through THF-dependent chemistry. (klein2022unravellingformaldehydemetabolism pages 4-5, wittmiss2020stoichiometryoftwo pages 1-2)

8.3 Subcellular localization

Consistent with THF-dependent one-carbon chemistry and soluble multi-enzyme complex function, the AM1 GcvT is expected to be cytosolic. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23)

9. Evidence table (compact annotation aid)

The following table summarizes the functional annotation in a compact form, including reaction logic, cofactors, pathway context, and quantitative data available from recent studies.

Gene/protein target	Protein name	EC number	Reaction / biochemical role	Main substrates/products	Cofactors / partner components	Pathway context in Methylorubrum extorquens AM1	Cellular localization	Key evidence notes	Key quantitative data	Key citations, URLs, dates
gcvT (UniProt C5AUG2; locus MexAM1_META1p0622)	Aminomethyltransferase; glycine cleavage system T protein (GcvT)	2.1.2.10	Forward GCV direction: transfers the aminomethyl group from aminomethylated H protein to THF, releasing NH3 and generating 5,10-methylene-THF while converting H-protein to the reduced form; part of the overall GCS conversion of glycine + THF + NAD+ → 5,10-methylene-THF + CO2 + NH3 + NADH + H+. Reverse/rGCS overall: participates in glycine synthesis from 5,10-methylene-THF + NH4+ + CO2 + reducing power → glycine + THF. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23, liu2023turnaircapturedco2 pages 1-2)	Forward: aminomethyl-H protein + THF → methylene-THF + NH3 + reduced H-protein. Overall forward GCV consumes glycine, THF, NAD+. Reverse overall rGCS consumes 5,10-CH2-THF, NH4+, CO2, reductant to make glycine + THF. (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23, liu2023turnaircapturedco2 pages 1-2)	Requires tetrahydrofolate (THF) as one-carbon acceptor and functions with GCS P, H, and L proteins; H protein carries the lipoyl-bound intermediate, L reoxidizes/reduces the H-protein cycle in the canonical system. In engineered systems, chemical reductants such as DTT can replace the L-protein reduction step. (wittmiss2020stoichiometryoftwo pages 1-2, liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7)	Links the glycine cleavage system to the THF one-carbon pool. In methylotrophs such as M. extorquens AM1, H4F/THF-linked C1 metabolism feeds assimilation pathways including the serine cycle; more broadly, GcvT is also a core enzyme for the reductive glycine pathway used in synthetic C1 assimilation. (klein2022unravellingformaldehydemetabolism pages 4-5, wittmiss2020stoichiometryoftwo pages 1-2, liu2023turnaircapturedco2 pages 1-2)	Cytosolic bacterial enzyme (inference from bacterial GCS/THF metabolism and lack of membrane association in cited pathway descriptions). (wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23, liu2023turnaircapturedco2 pages 1-2)	Identity verification: literature support matches UniProt annotation for GcvT as the aminomethyltransferase/T protein of GCS, but organism-specific primary literature directly characterizing AM1 gcvT/C5AUG2 is limited in the retrieved set. Review evidence confirms that M. extorquens AM1 uses H4F-dependent C1 metabolism tightly connected to the serine cycle, consistent with a cytosolic GcvT role in THF-linked one-carbon transfer. General GCS sources define the T-protein reaction and complex role; recent synthetic-biology studies use the same enzyme function in reverse GCS/rGlyP implementations. (klein2022unravellingformaldehydemetabolism pages 4-5, wittmiss2020stoichiometryoftwo pages 1-2, patel2016expressionofclostridium pages 20-23, liu2023turnaircapturedco2 pages 1-2)	2023 re-engineered rGCS data: overall glycine synthesis step 5,10-CH2-THF + NH4+ + CO2 + NADH → glycine + THF + NAD+ had ΔrG' = -1.2 kJ/mol; replacing the canonical reduction with DTT gave ΔrG' = -8.0 kJ/mol for the redesigned glycine synthesis step. Optimized system reached ~75 μM/min glycine production at 60 μM engineered H protein vs <20 μM/min with wild-type H; produced 15.5 mM (~1.2 g/L) glycine in 3.5 h, with 78% carbon yield from formaldehyde and 31% from CO2; with gaseous CO2 under 0.2 MPa, glycine reached 3.0 mM (30% CO2) or 2.3 mM (10% CO2). These numbers describe the GCS module that includes the T protein, not AM1-native enzyme kinetics specifically. (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media 54c2569d)	Liu J, Zhang H, Xu Y, Meng H, Zeng A-P. Nature Communications (2023-05), https://doi.org/10.1038/s41467-023-38490-w (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media 54c2569d); Wittmiß M et al. The Plant Journal (2020-05), https://doi.org/10.1111/tpj.14773 (wittmiss2020stoichiometryoftwo pages 1-2); Klein VJ et al. Microorganisms (2022-01), https://doi.org/10.3390/microorganisms10020220 (klein2022unravellingformaldehydemetabolism pages 4-5); Patel M. thesis/manuscript on GCS/rGlyP (2016) describing T-protein function (patel2016expressionofclostridium pages 20-23)

Table: This table summarizes the verified identity, enzymatic role, pathway context, localization, evidence base, and quantitative data relevant to functional annotation of Methylorubrum extorquens AM1 gcvT (UniProt C5AUG2). It is useful as a compact evidence-backed annotation aid, while noting the limited organism-specific primary literature directly on AM1 gcvT.

10. Visual evidence (key figures)

Two figure crops from Liu et al. (2023) provide (i) a thermodynamic table for key steps including glycine synthesis and (ii) glycine production performance plots and yields, illustrating how GcvT-containing modules are leveraged for CO2-to-amino acid biomanufacturing. (liu2023turnaircapturedco2 media 54c2569d, liu2023turnaircapturedco2 media d220b323)

11. Limitations and interpretation for AM1-specific annotation

AM1-specific direct functional experiments (knockouts/phenotypes for gcvT, purified AM1 GcvT kinetics, localization experiments) were not present in the retrieved documents. Therefore, AM1-specific claims are stated at the level of conserved enzyme function and AM1 THF/C1 network context, not as AM1-specific experimental results.
The strongest recent quantitative data here come from engineered/reconstituted GCS systems, which support functional expectations and applications but do not substitute for native AM1 biochemical characterization of UniProt C5AUG2.

References (URLs and publication dates)

Liu J, Zhang H, Xu Y, Meng H, Zeng A-P. “Turn air-captured CO2 with methanol into amino acid and pyruvate in an ATP/NAD(P)H-free chemoenzymatic system.” Nature Communications. Accepted 27 Apr 2023, published May 2023. https://doi.org/10.1038/s41467-023-38490-w (liu2023turnaircapturedco2 pages 1-2, liu2023turnaircapturedco2 pages 5-7, liu2023turnaircapturedco2 media 54c2569d, liu2023turnaircapturedco2 media d220b323)
Wittmiß M, Mikkat S, Hagemann M, Bauwe H. “Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system.” The Plant Journal. May 2020. https://doi.org/10.1111/tpj.14773 (wittmiss2020stoichiometryoftwo pages 1-2)
Klein VJ, Irla M, López MG, Brautaset T, Brito LF. “Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy.” Microorganisms. Jan 2022. https://doi.org/10.3390/microorganisms10020220 (klein2022unravellingformaldehydemetabolism pages 4-5)
Yishai O, Bouzon M, Döring V, Bar-Even A. “In Vivo Assimilation of One-Carbon via a Synthetic Reductive Glycine Pathway in Escherichia coli.” ACS Synthetic Biology. May 2018. https://doi.org/10.1021/acssynbio.8b00131 (yishai2018invivoassimilation pages 6-8)

References

(wittmiss2020stoichiometryoftwo pages 1-2): Maria Wittmiß, Stefan Mikkat, Martin Hagemann, and Hermann Bauwe. Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system. The Plant Journal, 103:801-813, May 2020. URL: https://doi.org/10.1111/tpj.14773, doi:10.1111/tpj.14773. This article has 8 citations.
(patel2016expressionofclostridium pages 20-23): M Patel. Expression of clostridium acidurici 9a glycine cleavage system in escherichia coli for formatotrophic growth via reductive glycine pathway. Unknown journal, 2016.
(klein2022unravellingformaldehydemetabolism pages 4-5): Vivien Jessica Klein, Marta Irla, Marina Gil López, Trygve Brautaset, and Luciana Fernandes Brito. Unravelling formaldehyde metabolism in bacteria: road towards synthetic methylotrophy. Microorganisms, 10:220, Jan 2022. URL: https://doi.org/10.3390/microorganisms10020220, doi:10.3390/microorganisms10020220. This article has 82 citations.
(liu2023turnaircapturedco2 pages 1-2): Jianming Liu, Han Zhang, Yingying Xu, Hao Meng, and An-Ping Zeng. Turn air-captured co2 with methanol into amino acid and pyruvate in an atp/nad(p)h-free chemoenzymatic system. Nature Communications, May 2023. URL: https://doi.org/10.1038/s41467-023-38490-w, doi:10.1038/s41467-023-38490-w. This article has 67 citations and is from a highest quality peer-reviewed journal.
(liu2023turnaircapturedco2 pages 5-7): Jianming Liu, Han Zhang, Yingying Xu, Hao Meng, and An-Ping Zeng. Turn air-captured co2 with methanol into amino acid and pyruvate in an atp/nad(p)h-free chemoenzymatic system. Nature Communications, May 2023. URL: https://doi.org/10.1038/s41467-023-38490-w, doi:10.1038/s41467-023-38490-w. This article has 67 citations and is from a highest quality peer-reviewed journal.
(liu2023turnaircapturedco2 media 54c2569d): Jianming Liu, Han Zhang, Yingying Xu, Hao Meng, and An-Ping Zeng. Turn air-captured co2 with methanol into amino acid and pyruvate in an atp/nad(p)h-free chemoenzymatic system. Nature Communications, May 2023. URL: https://doi.org/10.1038/s41467-023-38490-w, doi:10.1038/s41467-023-38490-w. This article has 67 citations and is from a highest quality peer-reviewed journal.
(liu2023turnaircapturedco2 media d220b323): Jianming Liu, Han Zhang, Yingying Xu, Hao Meng, and An-Ping Zeng. Turn air-captured co2 with methanol into amino acid and pyruvate in an atp/nad(p)h-free chemoenzymatic system. Nature Communications, May 2023. URL: https://doi.org/10.1038/s41467-023-38490-w, doi:10.1038/s41467-023-38490-w. This article has 67 citations and is from a highest quality peer-reviewed journal.
(yishai2018invivoassimilation pages 6-8): Oren Yishai, Madeleine Bouzon, Volker Döring, and Arren Bar-Even. In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in escherichia coli. ACS synthetic biology, 7 9:2023-2028, May 2018. URL: https://doi.org/10.1021/acssynbio.8b00131, doi:10.1021/acssynbio.8b00131. This article has 203 citations and is from a domain leading peer-reviewed journal.
(xu2022improvementofglycine pages 1-2): Yingying Xu, Jie Ren, Wei Wang, and An‐Ping Zeng. Improvement of glycine biosynthesis from one‐carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro. Engineering in Life Sciences, 22:40-53, Nov 2022. URL: https://doi.org/10.1002/elsc.202100047, doi:10.1002/elsc.202100047. This article has 34 citations and is from a peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

wittmiss2020stoichiometryoftwo pages 1-2
patel2016expressionofclostridium pages 20-23
klein2022unravellingformaldehydemetabolism pages 4-5
yishai2018invivoassimilation pages 6-8
xu2022improvementofglycine pages 1-2
https://doi.org/10.1038/s41467-023-38490-w
https://doi.org/10.1111/tpj.14773
https://doi.org/10.3390/microorganisms10020220
https://doi.org/10.1021/acssynbio.8b00131
https://doi.org/10.1111/tpj.14773,
https://doi.org/10.3390/microorganisms10020220,
https://doi.org/10.1038/s41467-023-38490-w,
https://doi.org/10.1021/acssynbio.8b00131,
https://doi.org/10.1002/elsc.202100047,

📄 View Raw YAML

---
id: C5AUG2
gene_symbol: gcvT
product_type: PROTEIN
taxon:
  id: NCBITaxon:272630
  label: Methylorubrum extorquens AM1
description: 'gcvT encodes aminomethyltransferase (EC 2.1.2.10), also known as glycine
  cleavage system T protein, which catalyzes the final step of the glycine cleavage
  system: the transfer of the aminomethyl group from the lipoyl-bound intermediate
  (on gcvH) to tetrahydrofolate (THF), producing 5,10-methylene-THF and releasing
  ammonia. The enzyme belongs to the GcvT family and functions as a component of the
  glycine cleavage complex, working in concert with gcvP (P protein, glycine dehydrogenase),
  gcvH (H protein, lipoyl-carrier), and gcvL (L protein, dihydrolipoyl dehydrogenase).
  In methylotrophs, the glycine cleavage system connects the serine cycle to the THF
  one-carbon pool: glycine (produced from serine by serA) is oxidatively cleaved by
  the GCV system, generating 5,10-methylene-THF (which feeds into C1 metabolism),
  CO2, and ammonia. GcvT contains two characteristic domains: an aminomethyltransferase
  folate-binding domain (residues 25-274) and a C-terminal domain (residues 305-385).
  The enzyme is essential for glycine catabolism and for connecting amino acid metabolism
  to the THF-dependent one-carbon pool, allowing the organism to recycle one-carbon
  units between different pathways during methylotrophic growth.'
existing_annotations:
  - term:
      id: GO:0004047
      label: aminomethyltransferase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: This is the primary and specific catalytic activity of GcvT - the transfer
        of the aminomethyl group from the lipoyl-bound intermediate (on gcvH) to tetrahydrofolate,
        producing 5,10-methylene-THF and ammonia. [file:METEA/gcvT/gcvT-uniprot.txt,
        "aminomethyltransferase"; "N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein]
        + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]
        + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+)"]. Falcon deep research
        independently confirms this is the conserved, core catalytic role of GcvT across
        bacteria and corroborates the products of the reaction.
      action: ACCEPT
      supported_by:
        - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
          supporting_text: transfers the aminomethyl group from the H-protein intermediate
            to **THF**, producing **5,10-methylene-THF** and releasing **NH3**
        - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
          supporting_text: is a core catalytic component of the **glycine cleavage system**
  - term:
      id: GO:0005960
      label: glycine cleavage complex
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: GcvT is a component of the glycine cleavage complex, working together
        with gcvP, gcvH, and gcvL to catalyze the oxidative cleavage of glycine. This
        is the primary cellular location for the enzyme. [file:METEA/gcvT/gcvT-uniprot.txt,
        "Glycine cleavage system T protein"]. Falcon deep research confirms GcvT (the
        T protein) functions with the GCS P, H, and L proteins, with the H protein
        carrying the lipoyl-bound aminomethyl intermediate that GcvT acts on.
      action: ACCEPT
      supported_by:
        - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
          supporting_text: functions with GCS **P, H, and L** proteins; H protein carries
            the lipoyl-bound intermediate
  - term:
      id: GO:0006546
      label: glycine catabolic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: GcvT catalyzes the final step of glycine catabolism via the glycine
        cleavage system, transferring the aminomethyl group to THF and releasing ammonia.
        This connects glycine degradation to the one-carbon pool. [file:METEA/gcvT/gcvT-uniprot.txt,
        "Glycine cleavage system T protein"]. Falcon deep research corroborates that
        by producing 5,10-methylene-THF, GcvT links glycine interconversion to the
        one-carbon folate pool, which in Methylorubrum extorquens AM1 feeds assimilation
        pathways including the serine cycle.
      action: ACCEPT
      supported_by:
        - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
          supporting_text: By producing **5,10-methylene-THF**, GcvT links glycine interconversion
            to the **one-carbon folate pool**
        - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
          supporting_text: H4F-dependent enzymes help maintain high levels of intermediates
            needed to feed the assimilatory serine cycle
  - term:
      id: GO:0008483
      label: transaminase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: This is technically correct as GcvT transfers an aminomethyl group,
        but it's a somewhat misleading general term. The more specific term GO:0004047
        (aminomethyltransferase activity) provides better functional annotation.
      action: KEEP_AS_NON_CORE
  - term:
      id: GO:0016740
      label: transferase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: This is a very general parent term for all enzymes that transfer functional
        groups. While technically correct, the more specific term GO:0004047 provides
        much better functional annotation.
      action: KEEP_AS_NON_CORE
core_functions:
  - description: 'GcvT catalyzes the final step of the glycine cleavage system, transferring
      the aminomethyl group from the lipoyl-bound intermediate (on gcvH carrier protein)
      to tetrahydrofolate (THF), producing 5,10-methylene-THF and releasing ammonia.
      The enzyme functions as a component of the glycine cleavage complex, working
      in concert with gcvP (P protein), gcvH (H protein), and gcvL (L protein) to
      catalyze the oxidative cleavage of glycine. In the context of methylotrophic
      metabolism, the glycine cleavage system connects the serine cycle to the THF
      one-carbon pool: glycine (produced from serine) is oxidatively cleaved, generating
      5,10-methylene-THF that feeds into C1 metabolism, plus CO2 and ammonia. GcvT
      contains an aminomethyltransferase folate-binding domain and a C-terminal domain,
      and belongs to the GcvT family. The enzyme is essential for glycine catabolism
      and for recycling one-carbon units between amino acid metabolism and the THF-dependent
      one-carbon pool during methylotrophic growth.'
    molecular_function:
      id: GO:0004047
      label: aminomethyltransferase activity
    directly_involved_in:
      - id: GO:0006546
        label: glycine catabolic process
    supported_by:
      - reference_id: file:METEA/gcvT/gcvT-uniprot.txt
        supporting_text: aminomethyltransferase...Glycine cleavage system T protein...N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein]
          + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]
          + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+)
      - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
        supporting_text: transfers the aminomethyl group from the H-protein intermediate
          to **THF**, producing **5,10-methylene-THF** and releasing **NH3**
      - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
        supporting_text: By producing **5,10-methylene-THF**, GcvT links glycine interconversion
          to the **one-carbon folate pool**
      - reference_id: file:METEA/gcvT/gcvT-deep-research-falcon.md
        supporting_text: functions with GCS **P, H, and L** proteins; H protein carries
          the lipoyl-bound intermediate
    in_complex:
      id: GO:0005960
      label: glycine cleavage complex
references:
  - id: file:METEA/gcvT/gcvT-deep-research-falcon.md
    title: Falcon deep research report for gcvT (C5AUG2) in Methylorubrum extorquens
      AM1
    findings:
      - supporting_text: transfers the aminomethyl group from the H-protein intermediate
          to **THF**, producing **5,10-methylene-THF** and releasing **NH3**
        reference_section_type: OTHER
      - supporting_text: is a core catalytic component of the **glycine cleavage system**
        reference_section_type: OTHER
      - supporting_text: functions with GCS **P, H, and L** proteins; H protein carries
          the lipoyl-bound intermediate
        reference_section_type: OTHER
      - supporting_text: By producing **5,10-methylene-THF**, GcvT links glycine interconversion
          to the **one-carbon folate pool**
        reference_section_type: OTHER
      - supporting_text: H4F-dependent enzymes help maintain high levels of intermediates
          needed to feed the assimilatory serine cycle
        reference_section_type: OTHER
      - supporting_text: the THF-dependent one-carbon network and the GCS proteins are
          typically **cytosolic**
        reference_section_type: OTHER
      - supporting_text: the AM1 GcvT is expected to be **cytosolic**
        reference_section_type: OTHER
      - supporting_text: GcvT is also a core enzyme for the **reductive glycine pathway**
          used in synthetic C1 assimilation
        reference_section_type: OTHER
  - id: file:METEA/gcvT/gcvT-uniprot.txt
    title: UniProt entry for gcvT aminomethyltransferase
    findings: []
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with GO
      terms.
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods.
    findings: []
status: COMPLETE

gcvT

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

Research report: gcvT (UniProt C5AUG2) in Methylorubrum extorquens AM1 (METEA)

Executive summary

1. Target verification and disambiguation (critical identity checks)

1.1 UniProt-provided identity (authoritative anchor)

1.2 Gene symbol ambiguity management

2. Key concepts and definitions (current understanding)

2.1 The glycine cleavage system (GCS) and GcvT’s role

2.2 Reaction chemistry and substrate specificity

2.3 Cellular localization

3. Organism context: Methylorubrum extorquens AM1 and C1 metabolism

4. Recent developments (prioritizing 2023–2024) and latest research

4.1 2023 (highly relevant): engineered reversible GCS for CO2-to-amino acid synthesis

4.2 2024: limited direct GcvT-specific advances in retrieved set

5. Current applications and real-world implementations

5.1 Synthetic C1 assimilation (reductive glycine pathway) and pathway construction logic

5.2 Cell-free biomanufacturing: CO2-derived amino acids

6. Expert opinions and authoritative analysis (what the field considers important)

7. Relevant quantitative data and statistics (recent studies)

7.1 Thermodynamic and performance statistics for a GcvT-containing rGCS module (2023)

8. Functional annotation narrative (for METEA gcvT / UniProt C5AUG2)

8.1 Molecular function

8.2 Biological process and pathway assignment

8.3 Subcellular localization

9. Evidence table (compact annotation aid)

10. Visual evidence (key figures)

11. Limitations and interpretation for AM1-specific annotation

References (URLs and publication dates)

Artifacts

Citations

📄 View Raw YAML